My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been collecting 3 dimensional structures of the enzymes and annotating polymorphic amino acids. That part is very straightforward. The complicated part of the project is figuring out how the structures correspond to the genes, genetic data, and association studies with diverse polymorphisms.
Vaccines work by stimulating the immune system to respond to a specific thing. Most of the vaccines we use are designed to prime the immune system so that it's ready to fight off some kind of disease, like whooping cough, polio, or influenza. Some vaccines can have more specialized functions, like stimulating the body to attack cancer cells, kill rogue autoimmune cells, or prevent pregnancy. We'll look at what they do in later posts, for now, let's look at the kinds of things that can be used as vaccines.
A long time ago, I saw a movie called "The Other Side of the Mountain." The movie told the story of Jill Kinmont, a ski racer who contracted polio and lost the use of her legs. I was sad for days for afterward, but also relieved to know that Jill Kinmont's fate wasn't going to be mine. I wasn't going to wake up in an iron lung after a ski race, and neither were my friends, because most of the children in my generation had been vaccinated against the Polio virus.
This image shows a polio survivor learning to walk. The image comes from the CDC Public Health Image Library
Every year people adopt pet dogs, cats, birds, and other creatures and take them to their local veterinarians for all the usual vaccinations and exams. The usual vaccinations protect your pets from diseases like rabies, distemper, Feline Immunodeficiency Virus, and Feline Leukemia. But it's not just pets that get protected by vaccines. Agricultural creatures: fish, chickens, sheep, cows, pigs, and horses receive vaccines and increasingly, wild animals are getting vaccinated, too.
Wanna change the world? Make it possible for everyone to talk about science in a normal conversation? Do you have ideas for improving science literacy?
Seed is interested in your ideas. Answer the survey and share your thoughts. And I've seen the MacBook Air. It's beautiful.
UPDATE: if you had trouble accessing the survey, try it again. It will be open until Friday, August 15th, 11pm EST.
write your Senators and Representatives about saving the Endangered Species Act.
But, first read what Mike Dunford has to say. Mike describes the changes that the Bush administration has proposed in great detail and consequences for wild animals. Greg Laden has posted on this, too.
Ancestry tests aren't just for humans anymore. We went to Petco this weekend to buy dog food and found brochures for doggy DNA testing. Now, those of you with dogs of uncertain parentage need puzzle no longer. According to Petco, their SNP test (what is a SNP?) can identify over 100 different breeds and they'll tell you which breeds are represented in your dog and whether your dog's breeding is mixed (or pure).
The first lab mouse I touched had soft white fur and a light pink tail. It looked cute enough to snuggle and take home as a pet and I was smitten. I slipped my hand into the cage, thinking the mouse would respond like my pet gerbils or my brother's pet rat. As my hand closed around its belly, that sweet little mouse sunk its teeth deep in my thumb. I screamed and shook my hand, smashing the mouse on the cement floor and killing it in an instant.
Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August?
Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'.
A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning.
Only, it turned out that when I looked at the gene map...
"Did you know," my friend whispered, "that the Humane Society funds terrorists?"
I was stunned. What? That's crazy! I've adopted pets from there. No way! How could those be the same people??
My friend and I were suffering from "brand confusion." In business, this happens when different companies use similar names for their products in order to confuse the marketplace. In the animal rights movement, brand confusion is used to misdirect the funds that would otherwise help groups who do genuine humanitarian work.
As I learned in "The Animal Research War" by P. Micheal Conn and James Parker [published by Palgrave Macmillan, ISBN-13:978-0-230-60014-0], there is an animal rights group that goes by the name of the Humane Society of the United States (HSUS). But this is not the group that runs animal shelters. The HSUS takes the money that well-meaning people think they're giving to shelters and uses it to fund propaganda campaigns. Unlike the other humane societies, this group is aligned with those who find it acceptable to firebomb homes.
Leave it to those wacky Korean cloners. In December, scientists from Gyeongsang National University gave us fluorescent kitties. Now, we have cute little puppies!
These aren't the first cloned pets on the market, we have stores that sell glowing fish. But these clones have a bit higher price tag. For $50,000 Bernann McKinney got 5 new "Boogers" from RNL Bio; "Booger McKinney," "Booger Lee," "Booger Ra," "Booger Hong and "Booger Park." That's $10,000 a Booger!
Still, who can resist these cute little boogers? I have a picture of the puppies below the fold and as you can see, they're adorable!
When female bloggers get death threats for comparing a Batman movie to a poor business plan, and friends can have their lab fire bombed for doing plant genetics, it's sometimes a little scary to step into the fray and take a stand on controversial issues.
But that's the point. We have to speak out. Scary or not, unless we speak out against the animal rights terrorists who firebomb people's homes and harass researchers, we will lose any chance to save our loved ones from diseases like cancer, HIV, Alzheimer's, or many others.
Microbiologist develop some strange habits when it comes to food.
Some take a fatalistic approach. They reason that microbes are everywhere, we're going to die anyway, we might as well eat dirt and make antibodies. You know these people. They quote things like the "10 second rule" when food drops on the floor, tell you we're all getting asthma because we're too obsessed with cleanliness, and let their dogs wash their dishes.
Eeew.
With a few possible exceptions, I'm in the other camp.
This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
MDRNA Inc., a Puget Sound area company formerly known as Nastech, announced on Monday that they'd be laying off 23 people including their president and chief business officer. This might not sound like a lot, but according to Joseph Tartakoff, from the Seattle PI, this brings the total number of layoffs up to 145 since November.
These events present a challenge to those of us who teach in biotech programs or biotech-related fields. Nastech, the predecessor to MDRNA had been around for over 20 years. Who would expect a 20+ year company to shed three quarters of it's employees in a few short months?
This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence.
How well did the sequencing work?
Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two categories: technical and biological.
What happens when high school students clone and sequence genomic DNA?
Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
Pfizer has pledged to donate up to $10,000 to the cause of science education, through Donorschoose.org, but only if enough of you, dear readers go to Big Think: Think Science Now and vote for your favorite video.
If you're not familiar with Pfizer, they're a pretty well-known drug company. You probably read about one of their products every time you delete messages from your e-mail in-box.
You don't even have to watch the videos, just vote.
I strongly recommend watching the videos, though. They are all profiles of scientists who work at Pfizer or other research organizations. It's pretty interesting to hear their stories and learn about their careers.
The fund raiser will have a limited shelf-life, but hopefully BigThink will keep the profiles up for a while. This is a great resource for providing students a snapshot of scientists and their careers. I'm also impressed with Pfizer for profiling the most diverse group of scientists that I've ever seen outside of a real lab.
Next week you can satisfy your curiosity and learn about the personal genomics frontier at the same time.
Bertalan Meskó announced that Erin Davis (science writer) and Joyce Tung (human geneticist) from 23andMe will be giving a presentation next week in Second Life on personalized genetics.
"Let this sleepin' dog lie, son. Dog-gone it, I'm dog tired. I'm tired of leading the dog's life and fightin' likes cats and dogs against cats and dogs, a young pup's doggin' my trail tryin' to become top dog. I'm going to the dogs in a dog eat dog world, son. I... I'm so far over the hill... I'm on the bottom of the other side. "
- Wylie Burp from Fievel Goes West
I don't know why I find these stories about cloning puppies so interesting, but...
It's pretty common these days to pick up an issue of Science or Nature and see people ranting about GenBank (1). Many of the rants are triggered, at least in part, by a wide-spread misunderstanding of what GenBank is and how it works. Perhaps this can be solved through education, but I don't think that's likely. People from the NCBI can explain over and over again that some of the sequence databases in GenBank are meant to be an archival resource (2), and define the term "archive," but that's not going to help.
Confusion about database content and oversight is widespread in this community with good reason.
Right or wrong, the word "dopamine" always conjures up images in my head of rats pushing levers over and over again, working desperately hard to send shots of dopamine into their tiny little rodent brains.
One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI.
In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all know people who aren't deterred by the idea of punishment. We all know people who never seem to learn.
Could there be a physical reason, hidden in their genes?
Pets are funny things. Some owners find their pets to be closer than some human friends, other owners never really bond with their pets at all.
BioArts, a California biotech company, founded by ex-CEO of the now defunct Genetic Savings & Clone, is counting on the strength of those human-dog emotional bonds .
A few months ago, I made a new page for a more complete blogroll. Now, that my class is over and I have a break from traveling around leading workshops, I'm ready to add some links.
Other bloggers; Bora, Mike the Mad, PZ, Janet, DM, and Abel; use a nice technique called "blogroll amnesty" where they offer other writers a chance to be on their blogroll. I like that.
Students in the United States take many convoluted and unnecessarily complicated paths when it comes to finding careers in biotechnology. If Universities and community colleges worked together, an alternative path could benefit all parties; students, schools, industry, and the community.
The image below illustrates the current paths and the approximate time that each one takes.
Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog.
It also looks like he's looking for post-docs (see the side bar on the right of this page.)
Have you ever wondered what kinds of viruses can be found in human waste?
Mya Breitbart and team have been sequencing nucleic acids from fecal samples in order to find out. You might expect that we'd find viruses that infect humans or viruses that infect the bacteria in our gut.
I wouldn't have expected to learn the result that they found.
I'm in Berkeley right now at the annual Bio-Link Summer Fellows forum. We're getting to hear talks from people in the biotech industry, listen to enthusiastic instructors describe their biotech programs and ideas, and try out new educational materials.
Yesterday, two speakers (Damon Tighe and Jason Baumohl) from the Joint Genome Institute in Walnut Creek, CA, gave a fun talk about DNA sequencing and sequence assembly.
They also showed some very nice Flash animations, made by Damon Tighe, at the JGI, that illustrate how DNA sequencing is done. There's no sound, but the animations are quite nice. The site also has some step by step diagrams describing the process.
I think the animations and diagrams would be a great help to students who are engaged in DNA sequencing projects.
A little over ten years ago, Dr. Elaine Johnson obtained funding from the National Science Foundation to start Bio-Link, an Advanced Technology Education center, focused on biotechnology. Since that time, Dr. Johnson has become a national leader in biotech education, enlisting the country's top educators and industry captains to ensure that community college students receive a quality education and the best preparation possible for entering the workforce.
In this radio interview from Tech Nation, Dr. Johnson talks with Dr. Moira Gunn about the easiest way to a biotech career.
In part I, I wrote about my first semester of teaching on-line and talked about our challenges with technology. Blackboard had a database corruption event during finals week and I had all kinds of struggles with the Windows version of Microsoft Excel. Mike wrote and asked if I thought students should be working more with non-Microsoft software and what I thought the challenges would be in doing so.
I can answer with a totally unqualified "it depends."
This month's edition of Medicine 2.0 focuses on connections. You'll learn how new technologies are empowering patients by connecting them with their own health records, connecting patients and paramedics with doctors, and connecting doctors with each other.
For aspiring technicians, who live in the right parts of the country, biotech jobs are out there and waiting. But what if you don't want to be a technician? Or what if you're in graduate school, in a post-doc, or have a Ph.D. and simply want to do something else?
Where do you begin?
How do you know what sorts of positions are going to be a good match for your skills and talents? Is the outlook really as bleak as it may seem?
I got my copy of "A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As soon I skimmed through it and read some of the questions and answers, I knew this would be the kind of quick reference that I would like to have sitting above my desk.
RFLP is an acronym that stands for "Restriction Fragment Length Polymorphism." That's quite a mouthful and once you've said this phrase a few times, you realize why we use the initials instead.
I know a Restriction Fragment Length Polymorphism sounds like something that must be impossibly complicated to understand, but if we take the name apart, it's really not so bad.
"Why won't biotech companies hire people with Ph.D.s to be technicians?"
"I already have a Ph.D., how do I find a job?"
These were some of the questions that commenters left after my earlier posts (here, here and here) on biotechnology workforce shortages.
Unfortunately, for these students and post-docs, the shortfall of employees in the biotech industry is largely a shortfall of technicians. It is a sad thing that promoting science careers can have the unintended consequence of creating a surplus of unhappy post-docs and even more unhappy graduate students. Perversely, many of the efforts to expand and improve science education often don't reach the students who'd be happy to be technicians. Both groups get misled by the incorrect notion that science jobs require a Ph.D.
I'll tackle the job searching question in a later post, for now, let's focus on why it is that having a Ph.D. could make job searching harder.
After leading the Human Genome Project and the National Human Genome Research Institute at the NIH for many years, Francis Collins is retiring.
No matter what you think of Francis Collins, he's been successful in getting the genome project done and he's done some amazing things during the 15 years that he's headed NHGRI.
My friend, Dr. Joan Messer, told me many times about the hours he spent talking with students at one of the AAAS meetings. I will always remember him from the NWABR fund-raising dinner where he pulled out his guitar and had the entire audience singing about DNA.
On-line courses were a still a new phenomenon when I was teaching full-time. Our school was pretty gung-ho about on-line education but many instructors were skeptical, some were still lamenting having to learn how to use a computer and losing the services that used to be provided by departmental secretaries. Other instructors simply distrusted the entire idea, seeing distance learning as the equivalent of an educational scam, a kind of "get rich quick scheme" that would allow the school to collect more tuition dollars without paying instructors.
I never did teach an on-line course during my years as a tenured faculty member but I did take an on-line class in on-line teaching.
Where have all the flowers gone?
Long time passing
Where do all the flowers gone?
Long time ago
Where do all the flowers gone?
Young girls picked them everyone,
When will they ever learn? When will they ever learn?
- Pete Seeger
Where do graduate students and post-docs go when they decide it's time to leave the pipeline? And, if they're thinking about going, how do they find a path into something new?
In part I, I wrote about the shortage of technicians in the biotechnology industry and the general awareness that this problem is getting worse. This part will address the challenge of getting more students into programs that will prepare them for jobs in the biotech field. I've also been asked to write a bit more about finding jobs in companies, that post will be a bit later. Before proceeding, there are two points that need a bit of discussion. The first point is the whether there's a shortage at all and the second applies to the kind of shortage.
It's hard to see the forest when you're deep in the woods
Biotech workforce shortages are not distributed evenly. When you live in an area where companies are laying off large numbers of people, the idea of a shortage is a bit difficult to accept. Certainly, the people in Rhode Island might be skeptical. When a large employer like Amgen cut 20% of the local work force last fall, 300 people ended up on the streets looking for work.
Students, teachers and scientists converge tommorrow morning from all around the Puget Sound region and elsewhere in Washington to share their experiences and talk about science. The students will present posters, science-themed music, art, drama, and many different types of projects that involved first-hand research and investigation. Scientists from the local biotech companies and research institutions talk with the students and judge the projects.
The public viewing time is tomorrow, May 28th, between 9 am-12 noon at the Meydenbauer Center. More information can be found here.
This video is a great snapshot of a Biotech Expo from the past.
On June 1st, I'll be hosting the next edition of Medicine 2.0, a carnival devoted to exploring the impacts of web 2.0 technologies on medicine and medical practice.
All topics that consider the impacts of web 2.0 on medicine and healthcare are fair game.
Are you talking with doctors about sexually transmitted diseases in Second Life?
Have you had your genome sequenced? Do your doctors send you e-mail?
Are you using web technologies to measure your food consumption and calorie burning?
If you have an article that you think fits the description, feel free to submit it to me, either via e-mail digitalbio at gmail.com or through the fancy blog carnival submission form.
Workforce shortages are a growing problem in the biotech industry. Communities are concerned that a lack of trained workers will either keep companies away or cause companies to move. If companies do have to move, it's likely those jobs might be lost forever, never to return. According to Robert Reich, former U.S. secretary of labor, now a professor at UC-Berkeley, biotech companies that can't hire in the U.S. will recruit foreign workers or open research centers overseas (Luke Timmerman, Seattle PI).
If I like what I see, I'll receive 5 more issues (6 in all) for just $14.95. That's 50% off the cover price! If I'm not completely satisfied, I'll simply write "cancel" on the invoice and owe nothing. The free issue is mine to keep.
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (
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Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the NCBI with the term 'August'.
Pets are funny things. Some owners find their pets to be closer than some human friends, other owners never really bond with their pets at all. 
Play
Nothing connects like Web 2.0.
My friend, Dr. Joan Messer, told me many times about the hours he spent talking with students at one of the AAAS meetings. I will always remember him from the NWABR fund-raising dinner where he pulled out his guitar and had the entire audience singing about DNA.
